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USER MANUAL FOR THE IDEA EBV INTERFACE

Preface

The following is a manual to guide the user through the features of the new IDEA. IDEA stands for Interbull Data Exchange Area. IDEA is a restricted area accessible only to member countries through the Interbull website.

Software menu

The Software menu gives you access to the Interbull checking programs. By clicking on Software a drop down menu will open and you will be able to choose the type of checking program you are interested in, i.e. Pedigree or Proofs. Under Software you will also find information on the programs and instructions on how to run them.

Proof's Checking Program

A Python program called CheckProofsPara.py will check the 300/700 proof file format and the associated 301/701 parameter file for format correctness against IDEA (Appendix I+Appendix II.) The program prepares a zip file, IB-ORGCODE-IG-yyymmddThhmmss.zip for conventional MACE and IB-ORGCODE-GG-yyymmddThhmmss.zip for GMACE,if no errors are found in the file. The zip file represents your checked data file to upload to the Interbull Centre IDEA database (https://idea.interbull.org/).

The user instructions (https://wiki.interbull.org/public/CheckProofPara#preview) for the CheckProofsPara.py program and file formats (see Appendix I and II) give details on how to run the program and on the checks performed.

Proofs menu

The Proofs menu gives you access to the main proofs functions which are:Upload, Review, Messages.

Upload and Verify program

By uploading data in IDEA users will no longer need to run the Verify program prior sending data to Interbull Centre. The Verify program will, in fact, be run automatically in IDEA during uploading.

Uploading functionality for parameter and proof files are available under 'Proofs/Upload'. The only file accepted by IDEA is the zip file IB-ORGCODE-XG-yyymmddThhmmss.zip produced by the CheckProofsPara.py, no other files are accepted. Once in 'Proofs/Upload' users will be able to browse the appropriate file and upload it by click on "Submit query".

The uploading of data will not happen on real time but data will be set on a queue and processed on a later time. Right after clicking "Submit query" a message on the screen will display the amount of parameter and proofs records submitted. A confirmation email will be sent to the email address associated to the user that has uploaded data.
The following are the steps the data will go through during uploading:

  1. CheckProofsPara.py will run once again inside IDEA to assure correctness of format and contents

  2. The Verify program will check your data against the previous one available.

Confirmation email

Either an "EBV upload success" or an "EBV upload error" email will be sent to you upon completion of the uploading process.

Upload successful

If the uploading is successful the "EBV upload success" email will list some basic information on your data such as:

The email can contain up to three different WARNINGS. The three first warnings below are associated to attachments and requires actions which are described in the actions for attachment table below:

  1. Warning: [n] animal(s) were referenced in your file, but not present in the pedigree database. These animals were discarded! See a detailed list in the attached 'missing_animals.csv' file.
  2. Warning: [n] animal(s) needing updated pedigree records detected! See 'ped_needed.csv' for a complete list of the animals.
  3. Warning: Use of aliases detected! See 'ped_alias.csv' for a complete list of the animals.
  4. This warning is generated if the uploaded file contains re-uploadings for a given Breed-Pop-Trait combination which have not been withdrawed first (see Withdraw data):
    • WARNING: This dataset re-uploads already existing data, of which some has not been withdrawn first. These combinations have been skipped; the proper way to re-upload combinations is to withdraw them first (or ask IBC staff to reset them). These combinations have been skipped:[......]

An important source of information comes from Number of flagged rows in proof file: this number represents the amount of discrepancies found by the Verify program. If it is 0 (zero) it means that no discrepancies have been found in your data. Please note that the data IS NOT AUTOMATICALLY submitted. After uploading to IDEA the data has to be submitted in the Proofs/Review page. If it is not 0 (zero) it means that the Verify program has found some discrepancies in your data compared to the previous one available or the system has detected animals with missing pedigree. To double check the data you need to log in IDEA and go to Proof/Review.

Actions for attachments

Animals not present in IDEA pedigree or lacking pedigree information (i.e. present in the pedigree database but with sire and dam unknown) will be excluded from the international evaluation.

Table 1 summarizes the action needed upon reception of a confirmation email with warnings and/or attachments:

Attachments

Meaning

Action Required

Consequences

missing_animals.csv

The animals listed in this attachment are not present in IDEA pedigree

Log in IDEA,
go to Proofs/review,
withdraw the data file,
prepare a file200 for these animals,
upload the file in IDEA pedigree,
after reception of the pedigree confirmation email upload again the proof file

If pedigree is not provided, animals are excluded from the international evaluation

ped_needed.csv

The animals listed in this attachment have sire/dam set to unknown

If you have pedigree information for these animals:
log in IDEA,
go to Proof/review,
withdraw the data file,
prepare a file200 for these animals,
upload the file in IDEA pedigree,
after reception of the pedigree confirmation email upload again the proof file.
If you don't have such information you can submit the file: you will be asked to write an explanation

If pedigree is not provided, animals are excluded from the international evaluation

ped_alias.csv

The animal IDs listed in this attachment are alias IDs

You are requested to update your own database with the correct animals' IDs.

Alias IDs are automatically switched to their corresponding official IDs.

Refer to the section 'Submit/Withdraw data' for more information

Upload not successful

There can be three main reasons for an uploading to fail, the different reasons are descripted in the specific "EBV upload error" email you could receive. The table below presents and explaine each of the possible cases:

Email content

Meaning

Action Required

'System internal error. This should usually not happen. Contact staff for clarification'

Technical problems with the database server

contact Interbull Centre

'The data already exists in the database and no combinations were updated due to not having the right status for re-uploading; the proper way to re-upload combinations is to withdraw them first (or ask IBC staff to reset them).'

The content of the file was not uploaded

Log in IDEA,
go to Proofs/review,
withdraw the specific breed-trait combinations present in the file
re-upload the file

'Formal correctness errors were encountered in the uploaded file'

The file was not uploaded due to format errors

Review the file with the CheckProofPara
re-upload the file


Review your data

General

Uploading represents only the very first step for submitting your data for an IGE. Here is a description of the actions you need to follow to submit your data for an IGE. The Proof/Review page contains all the information you need to review and submit your data for a IGE.

The page contains several important information grouped into three different tables: Filters table, Central (Include) table and Actions table

Filter table

The Filters table allows you to filter and display the information you have uploaded in a way that better suits you. By default the Central (Include) table displays all the information associated to your account but you can costumize the displaying of information choosing among:

Clicking "Reset all" will erase all your previous filters and display again all the information associated to your account.

review1.png

Central (Include) table

The Central (Include) table displays as many rows as the breed-pop-trait combinations you have uploaded. Each row shows the following information:

The Breed-Pop-Trait combinations not highlighted and with Flagged=NO are combinations for which the Verify program did not find any discrepancies, nevertheless they will still get a status= Pending as your final approval on the data is still required.

The Breed-Pop-Trait combinations highlighted in yellow require your attention. For each of them you need to check the Verify output. For your convenience, selecting such combinations and clicking on "View Summary for Selected", located at the end of the Central table, will display in a new page the main key checking points of the Verify output. You can select the combination either manually, by clicking in the box in the "include" column, or by clicking on "Reverse selection".

Actions table

The Actions table displays the options you have for your data with status=PENDING. You can decide to submit or withdraw such data by selecting the desired action and clicking on "Submit".

Submit data

If, after checking the Verify output ,you consider your data to be ok and want to include it in the IGE you can do so by selecting the box beside each Breed-Pop-Trait combination you want to include, select the action "Submit" and click on the "Submit" button.

Every time you submit a pending data you are required to explain the reasons for the discrepancies found by the Verify program. If the reason are breed-trait dependent you need to processed these cases one by one and provide the full explanation in the designed space "Change comment". If, on the other hand, the same explanation applies to several Breed-Pop-Traits combinations you can select them together in the Review page so that you will be required to write only once the explanation that all these data share.By clicking "Send message" your message will be recorded under IDEA Proofs/Messages and will be visible by you and the Interbull Centre Staff.

In the Review page, the Breed-Pop-Trait combinations you have submitted will be now displayed with status=Submitted.

On the day of the data submission deadline for a given IGE, routine or test run, all your data in the Review page should have status=SUBMITTED. Your aim is therefore to check all pending data and either provide explanations or withdraw and upload new datasets before the data submission deadline.

Submit_pending.png

Withdraw data

If you realize the data you have uploaded for some Breed-Pop-trait combinations is wrong or you want to upload pedigree information for the animals reported in the confirmation email attachments you need to withdraw your data before doing anything else. You do so by simply selecting the affected Breed-Pop-Trait combinations in the Review page, select the action Withdraw and then press the button "Submit".In the Review page that given Bredd-Pop-trait combination will now have status=WITHDRAWED.

When you withdraw a given Breed-Pop-Trait all records present in IDEA for that combination are deleted thus you have to re upload the file before the data deadline. It is not acceptable to submit a partial dataset in order to correct the evaluations of some subset of bulls. It is essential that proof records for all bulls be included in the same file for any one brd-pop-trt combination whether the dataset is a first submission for the IGE run in question, or a re-submission with some problem corrected.

If you fail to withdraw all the traits you are going to re-upload in a new file, the confirmation email will contain the following warning:

Example:
You notice some problem with the temperament data for RDC. You withdraw only the RDC-Tem from your Review table and in the new file to upload you also include data for RDC msp. As you did not withdraw the RDC-msp combination before uploading the new file, all the combinations referring to RDC-msp are skipped as data already exist in IDEA for that given combination.

Accepted/Rejected

Once you have submitted your data for a given IGE it will be up to the ITBC staff to finally accept or reject it. In general all data with FLAGGED=NO will also get accepted as there are no issues pending on these data. For all the data with FLAGGED=YES, ITBC staff will go through the explanations you have reported and if found sufficients will mark that given Breed-Pop-Trait combination as accepted. If more clarifications are needed ITBC staff will email you via IDEA, anytime a new message will be posted in your IDEA account by the staff you will receive an email informing about the presence of unreplied messages in IDEA.

In case the discrepancies found are considered too big then ITBC staff can reject your data and use the data from the previous run. You will be able to follow what happens to your data by looking at the Review page as the status will change according to what decision has been made.

Messages

Proofs/Messages represents the place where all your communication with the ITBC for a given IGE are displayed. All the explanations you provide for a given Breed-Pop-Trait combination are automatically listed in here. Unreplied messages will be marked in red. You can use this page to send further messages to ITBC staff. When ITBC staff replies, their messages will also be listed here and you will be notified by email about the presence of unreplied messages in IDEA.

messages.png

Message Overview

In the message overview you can review all the communications you had with the staff for any given evaluation.

By selecting the evaluation you are interested in and pressing "Set Run", all messages exchanged between you and the ITBC staff during the evaluation you have selected will be listed in a table.

Proof Query

Proofs/Proof Query gives you the possibility to look up proof records associated to a given animal ID; you can filter the search to a specific runid or retrieve the information available for that ID in all the run id available in the database as well as filter it by population, traits or trait group. Once you have selected your filters and press "Search" two tables will be displayed: an animal information table showing the pedigree for that animal and a second table with information on: run id, breed, population, trait, type of file (Conventional or Genomic), type of proof, publication, status of bull, number of daughters, number of herds, EDC, reliability and proof. The heading of the second table is an active heading, this means that by clicking on it you can sort the content of the table.

Through the Proof Query you will be able to look up only the animals that have been submitted by your organization.

proof_query1.png

Parameter Query

Proofs/Parameter Query gives you the possibility to look up parameter records associated to a given run ID or retrieve the cases where the parameter records differ; you can filter the search to a specific run id or by breed, population, traits or trait group. Once you have selected your filters and press "Search" a table will be displayed with information on: run id, breed, population, trait, type of file (Conventional or Genomic), evaluation date, base definition, genetic merit, publication rule, heritability. The heading of the table is an active heading, this means that by clicking on it you can sort the content of the table.

Through the Parameter Query you will be able to look up only records that have been submitted by your organization.

query_param.png

Handling of cross-reference and alias' proofs

When a cross-reference link is created in the pedigree via uploading of a file202, the new official ID will retain its own proofs as well as acquire the proofs of the alias ID for those combinations it didn't have previously.


APPENDIX I - Format File300-EBV and File700-GEBV

Col

Name

Start

Format

Description

Example

1

rec type

1

a3

Record type 1

300

2

brd_eval

5

a3

Breed of evaluation 2

HOL

3

pop

9

a3

Population code 3

USA

4

trt

13

a3

Trait of evaluation 4

mil

5

brd_anim

17

a3

Breed of animal

HOL

6

cou_orig

20

a3

Country of first registration

USA

7

sex

23

a1

Sex of animal

M

8

id_no

24

a12

Animal identification number

003000336289

9

typ_prf

37

i2

Type of proof 5

11

10

off_pub

40

a1

Official publicationof proof 6

Y

11

status

42

i2

Animal status 7

10

12

ndau

44

i8

Number of daughters 8

115

13

nhrd

52

i8

Number of herds 9

75

14

edc

60

i8

Number of effective daughter contributions 10

133

15

rel

69

f7.4

Repeatability/Reliability 11

82

16

ebv

76

f10.

National predicted genetic merit 12

2.780

  IMPORTANT NOTE !!!!!

  In the old fileformat 01x-020 and 115, the national proofs were multiplied by a factor: (prod=100; conf=100;udder=1000;long=1000;calv=1000;fert=1000; fert=1000;work=1000).  This multiplication will no longer be needed.
  • 1Valid record types:

    • 300 for EBV
    • 700 for GEBV
  • 2Breed codes accepted:

    • BSW=Brown Swiss type; GUE=Guernsey type; HOL=Holstein-Friesian (Black & White) type; JER=Jersey type; RDC=Red Dairy Cattle type ; SIM=Simmental type.

  • 3Valid population codes: ARG AUS BEL CAN CHE aCHR CZE bDEA DEU cDFS dDNR ESP EST FIN FRA eFRM fFRR GBR HUN IRL ISR ITA JPN LTU LVA NLD NZL POL PRT SVN SVK SWE USA URY ZAF

    • where: aSwiss Red Holstein; b Austria+Germany; cDenmark + Finland + Sweden; dDenmark Red Holstein e France Montbeliarde; fFrench Pie Rouge

  • 4Accepted traits abbreviations:

    • Production ==> mil = milk;fat =fat; pro = protein;

    • Conformation ==> sta = stature;cwi = chest width;bde = body depth;ang = angularity;ran = rump angle;rwi = rump width; rls = rear-leg set;rlr = rear-leg rear view;fan = foot angle;hde = heel depth/hoof height; fua = fore udder attachment; ruh = rear udder height; ruw = rear udder width; usu = udder support;ude = udder depth;ftp = front teat placement;ftl = (front) teat length;rtp = rear teat placement;ous = overall udder score; ofl = overall feet&legs score; ocs = overall conformation score; bcs = body condition score; loc = locomotion;

    • Udder ==>scs = somatic cell; mas = mastitis

    • Longevity ==> dlo = direct longevity;

    • Calving ==> dce = direct calving ease;mce = maternal calving ease;dsb= direct stillbirth;msb = maternal stillbirth

    • Female fertility ==>hco = heifer conception;crc = cow recycling;cc1 = lactating cow's ability to conceive (1);cc2 = lactating cow's ability to conceive (2);int= internval traits

    • Workability ==> msp = milking speed;tem = temperament

  • 5Accepted codes:

    • 00 (unknown);

    • 11 (based on first crop sampling daughters);

    • 12 (based on first and second crop daughters);

    • 13 (based on parent average and genomic information only);

    • 21(based on imported semen of proven bull, second crop daughters only);

    • 22 (based on mostly, more than 50%, imported daughters or daughters born from imported embryos.)

  • 6Accepted abbreviations:

    • Y (if bull proof meets national standards for official publication in the country sending information.);

    • P (if bull is part of a simultaneous progeny-testing program, but the proof does not yet meet national standards for official publication);

    • N (otherwise).

  • 7Valid codes for status of bulls:

    • 00(unknown);

    • 10(bull randomly sampled through an official AI scheme);

    • 15 (young bull, genomically tested, not yet selected for AI);

    • 20(other bull. Records with “20” in this file will be excluded from the international evaluation, unless type of proof is “21”).

  • 8Field for number of daughters should be positive. For missing value put 0.

  • 9Field for number of herds should be positive. For missing value put 0.

  • 10 Production, conformation, udder health, fertility and workability traits: Weighting factor used for these traits is “the effective daughter contribution (EDC)”, which is described In the Interbull document Code of practice, Appendix IV, “Weighting factor for international genetic evaluation”, updated April 27, 2004. EDC values should be rounded to the nearest integer value.

    • Calving: The weighting factors used for calving traits it the total number of calvings for the direct effects and number of daughters with calving for maternal effect

    • Longevity: The weighting factor used for longevity traits depends on the national genetic evaluation model. For linear models the weighting factor is the same as described above for conformation, fertility, production, udder health and workability traits. For survival models number of culled daughters is used as the weighting factor.

  • 11Reliability values are nationally calculated reliability values expressed in percents with 4 decimials. For missing value put 0.

  • 12National predicted genetic merit values published domestically. For threshold models the submitted values are from the underlying scale. For missing values put 9999999999. Please note! In the old fileformat 01x-020 and 115, the national proofs were multiplied by a factor: (prod=100; conf=100;udder=1000;long=1000;calv=1000;fert=1000; fert=1000;work=1000). This multiplication will no longer be needed.


APPENDIX II - Format File301 - Parameters EBV and File701- Parameters GEBV

Col

Name

Start

Format

Description

Example

1

rec_type

1

a3

Record type 1

301

2

brd_eval

5

a3

Breed of evaluation 2

HOL

3

pop

9

a3

Population code 3

USA

4

trt

13

a3

Trait of evaluation 4

scs

5

evdate

17

i8

National evaluation date 5

20121201

6

herit

26

f8.6

Heritability 6

0.12

7

refbase

35

a7

Reference base definition 7

H10CB05

8

pgmdef

43

a2

Genetic merit definition 8

T-

9

pub_rule

46

a1

Official publication rules 9

Y

  • 1Valid record types:

    • 301 for EBV
    • 701 for GEBV
  • 2Breed codes accepted:

    • BSW=Brown Swiss type; GUE=Guernsey type; HOL=Holstein-Friesian (Black & White) type; JER=Jersey type; RDC=Red Dairy Cattle type ; SIM=Simmental type.

  • 3Valid population codes: ARG AUS BEL CAN CHE aCHR CZE bDEA DEU cDFS dDNR ESP EST FIN FRA eFRM fFRR GBR HUN IRL ISR ITA JPN LTU LVA NLD NZL POL PRT SVN SVK SWE USA URY ZAF

    • where: aSwiss Red Holstein; b Austria+Germany; cDenmark + Finland + Sweden; dDenmark Red Holstein e France Montbeliarde; fFrench Pie Rouge

  • 4Accepted traits abbreviations:

    • Production ==> mil = milk;fat =fat; pro = protein

    • Conformation ==> sta = stature;cwi = chest width;bde = body depth;ang = angularity;ran = rump angle;rwi = rump width; rls = rear-leg set;rlr = rear-leg rear view;fan = foot angle;hde = heel depth/hoof height; fua = fore udder attachment; ruh = rear udder height; ruw = rear udder width; usu = udder support;ude = udder depth;ftp = front teat placement;ftl = (front) teat length;rtp = rear teat placement;ous = overall udder score; ofl = overall feet&legs score; ocs = overall conformation score; bcs = body condition score; loc = locomotion

    • Udder ==> scs = somatic cell; mas = mastitis

    • Longevity ==> dlo = direct longevity

    • Calving ==> dce = direct calving ease;mce = maternal calving ease;dsb= direct stillbirth;msb = maternal stillbirth

    • Female fertility ==>hco = heifer conception;crc = cow recycling;cc1 = lactating cow's ability to conceive (1);cc2 = lactating cow's ability to conceive (2);int= internval traits)

    • Workability ==> msp = milking speed;tem = temperament.

  • 5 National evaluation dates expressed using the format YYYYMMDD

  • 6Heritability for a specific trait in format f8.6. Should be larger than 0 and smaller than 0,999999

  • 7 Reference (genetic) base definition in the country sending information: breed initial (1 char), year established (YY), bull(b) or cow(C) (1 char); birth(B), calving (C) or evaluation (E) (1 char); year of event (use middle year if base on multiple year (YY); for breed initial see breed code in footnote2 (use X If based on multiple breeds):e.g. H00BB95 means a base defined 2000 base on Holstein bulls born in 1995.

  • 8Genetic merit definition consists of a letter and a sign:

    • Sign: ‘+’ = Higher values are desirable, ‘-‘= Lower values are desirable

    • B = Breeding value

    • T = Transmitting ability;

  • 9 Allowed characters :

    • Y=Yes

    • N=No


APPENDIX III - Frequently Asked Questions

My data has been rejected, what can i do?

National data can sometimes be rejected from ITBC staff if changes in sire standard deviations between previous and current data are larger than 5% (in case of routine run), or if problems in the data are found. If your data get rejected it means that the previous available data will be used for the IGE. In case you are able to fix the problem(s), and the data deadline has not yet passed, you can try to upload a new corrected dataset. You will need to check the confirmation email, the verify output and submit the data in the Review page again.

I discovered a problem with a dataset with FLAG=NO, what do I do?

As long as status=PENDING you can always upload a new corrected dataset, the new upload will overwrite the previou one. If you discover the error after submitting the data, and if the data deadline has not passed yet, you need to inform the ITBC staff about the problem and the breed-pop-trait combination affected by it. ITBC staff will reset your data so that you will be able to upload a new file again. You will need to check the confirmation email, the verify output and submit the data in the Review page again.

public/IDEA_EBV_UserManual (last edited 2014-12-08 10:10:18 by Valentina)